Package: methylInheritance 1.31.0

Astrid Deschênes

methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Authors:Astrid Deschênes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]

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methylInheritance.pdf |methylInheritance.html✨
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NEWS

# Install 'methylInheritance' in R:
install.packages('methylInheritance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeschen/methylinheritance/issues

Datasets:
  • demoForTransgenerationalAnalysis - The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
  • methylInheritanceResults - All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
  • samplesForTransgenerationalAnalysis - All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).

On BioConductor:methylInheritance-1.31.0(bioc 3.21)methylInheritance-1.30.0(bioc 3.20)

biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencinganalysisbioconductorbioinformaticscpgdifferentially-methylated-elementsinheritancemonte-carlo-samplingpermutation

4.60 score 1 scripts 232 downloads 9 exports 103 dependencies

Last updated 4 months agofrom:9150e3e680. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-winNOTEFeb 15 2025
R-4.5-macNOTEFeb 15 2025
R-4.5-linuxNOTEFeb 15 2025
R-4.4-winNOTEFeb 15 2025
R-4.4-macNOTEFeb 15 2025
R-4.3-winOKFeb 15 2025
R-4.3-macOKFeb 15 2025

Exports:calculateSignificantLevelextractInfoloadAllRDSResultsloadConvergenceDatamergePermutationAndObservationplotConvergenceGraphplotGraphrunObservationrunPermutation

Dependencies:abindaskpassbbmlebdsmatrixBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodacodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayemdbookfansifarverfastsegformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmethylKitmgcvmimemunsellmvtnormnlmenumDerivopensslpillarpkgconfigplyrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrebusrebus.baserebus.datetimesrebus.numbersrebus.unicodereshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Inferring inheritance of differentially methylated changes across multiple generations

Astrid Deschênes, Pascal Belleau and Arnaud Droit

Rendered frommethylInheritance.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2018-11-30
Started: 2017-04-07